Microarray analysis of stalk-eyed fly lines selected for divergent eyespan

Eye-stalks of some flies exhibit extreme sexual dimorphism, but little is known about the genetic mechanisms producing variation in these ornamental traits. Therefore, we constructed an EST database of genes expressed in the developing eye-antennal imaginal disc of the highly dimorphic species, Teleopsis dalmanni, and used this set of genes to construct high density oligoarrays and compare patterns of gene expression between lines of flies selected for divergent eyespan. Microarray experiments using eye-antennal disc tissue identified over 350 genes with significant differential expression between male flies from lines selected for high and low relative eyespan but did not reveal any primary biological process or pathway that is driving the expression differences. Custom 4x44K Agilent arrays were designed for approximately 3600 unique genes. Each gene was represented by three 60 bp oligo probes and each probe was printed in triplicate on each array. Each oligoarray was hybridized with two biological samples labeled either with cy3 or cy5. Each sample came from 25 sets of eye-antennal imaginal discs that were dissected from gut-purged male larvae. Samples were from lines of flies that had been under directional selection on males to either increase or decrease relative eyespan for 65 generations. Dye labeling was switched between lines for every other array. Ratios of median intensities were averaged across probes for each gene and then analyzed by SAM to identify genes with differential expression between lines.